In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling

Production of oils and fats by oleaginous microorganisms with an emphasis given to the potential of the nonconventional yeast Yarrowia lipolytica

(2018) E. Carsanba et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Modulation of the Glycerol Phosphate availability led to concomitant reduction in the citric acid excretion and increase in lipid content and yield in Yarrowia lipolytica

(2018) Rana Sagnak et al.   JOURNAL OF BIOTECHNOLOGY

Functional genomics for the oleaginous yeast Yarrowia lipolytica

(2018) Kurt Patterson et al.   METABOLIC ENGINEERING

Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis

(2018) Mohammad Tajparast et al.   PLoS One

Metabolic engineering in the host Yarrowia lipolytica

(2018) Ahmad M. Abdel-Mawgoud et al.   METABOLIC ENGINEERING

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism

(2017) Kangjian Qiao et al.   NATURE BIOTECHNOLOGY

Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

(2017) Shuobo Shi et al.   Frontiers in Microbiology

Modelling microbial metabolic rewiring during growth in a complex medium

(2016) Marco Fondi et al.   BMC GENOMICS

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

(2016) Kyle R. Pomraning et al.   BMC GENOMICS

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Metabolic engineering of microbial competitive advantage for industrial fermentation processes

(2016) A. Joe Shaw et al.   SCIENCE

Standardized Markerless Gene Integration for Pathway Engineering in Yarrowia lipolytica

(2016) Cory Schwartz et al.   ACS Synthetic Biology

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

(2016) René M. Daer et al.   ACS Synthetic Biology

Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR–Cas9-Mediated Genome Editing in Yarrowia lipolytica

(2016) Cory M. Schwartz et al.   ACS Synthetic Biology

Single cell oil production on molasses by Yarrowia lipolytica strains overexpressing DGA2 in multicopy

(2015) Peter Gajdoš et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Logical transformation of genome-scale metabolic models for gene level applications and analysis

(2015) Cheng Zhang et al.   BIOINFORMATICS

Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains ofStreptomyces coelicolor

(2015) Minsuk Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

(2015) Mohammad Tajparast et al.   BMC Systems Biology

Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

(2015) Martin Kavšček et al.   BMC Systems Biology

Engineering of oleaginous organisms for lipid production

(2015) Jennifer Levering et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica

(2015) Kangjian Qiao et al.   METABOLIC ENGINEERING

The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica

(2015) Thomas M. Wasylenko et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Microbial lipid-based lignocellulosic biorefinery: feasibility and challenges

(2015) Mingjie Jin et al.   TRENDS IN BIOTECHNOLOGY

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

(2015) Kyle R. Pomraning et al.   PLoS One

The role of malic enzyme as the provider of NADPH in oleaginous microorganisms: a reappraisal and unsolved problems

(2014) Colin Ratledge   BIOTECHNOLOGY LETTERS

Enhanced lipid accumulation in the yeast Yarrowia lipolytica by over-expression of ATP:citrate lyase from Mus musculus

(2014) Huaiyuan Zhang et al.   JOURNAL OF BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production

(2014) John Blazeck et al.   Nature Communications

Advancing oleaginous microorganisms to produce lipid via metabolic engineering technology

(2013) Ming-Hua Liang et al.   PROGRESS IN LIPID RESEARCH

COFACTOR MODIFICATION ANALYSIS: A COMPUTATIONAL FRAMEWORK TO IDENTIFY COFACTOR SPECIFICITY ENGINEERING TARGETS FOR STRAIN IMPROVEMENT

(2013) MEIYAPPAN LAKSHMANAN et al.   Journal of Bioinformatics and Computational Biology

Efficient homologous recombination with short length flanking fragments in Ku70 deficient Yarrowia lipolytica strains

(2012) Jonathan Verbeke et al.   BIOTECHNOLOGY LETTERS

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

(2012) Nicolas Loira et al.   BMC Systems Biology

Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production

(2012) Mitchell Tai et al.   METABOLIC ENGINEERING

Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

(2012) Pengcheng Pan et al.   PLoS One

A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides

(2012) Zhiwei Zhu et al.   Nature Communications

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Phosphate-limitation mediated lipid production by Rhodosporidium toruloides

(2010) Siguo Wu et al.   BIORESOURCE TECHNOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Lipids from heterotrophic microbes: advances in metabolism research

(2010) Matyas Kosa et al.   TRENDS IN BIOTECHNOLOGY

Yarrowia lipolytica as a model for bio-oil production

(2009) Athanasios Beopoulos et al.   PROGRESS IN LIPID RESEARCH

Perspectives of microbial oils for biodiesel production

(2008) Qiang Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY